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Multiplexed Single Cell mRNA Sequencing Analysis of Mouse Embryonic Cells
Published on: January 7, 2020
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Combinatorial analysis of mRNA expression patterns in mouse embryos using hybridization chain reaction
David Huss1, Harry M T Choi2, Carol Readhead3
1Keck School of Medicine, University of Southern California, Children's Hospital Los Angeles, California 90027;
Cold Spring Harbor Protocols
|March 4, 2015
Summary
Multiplexed fluorescent in situ hybridization chain reaction (HCR) enables simultaneous detection of multiple gene expression patterns in mouse embryos. This advanced imaging technique provides high spatial resolution for studying complex developmental processes.
Area of Science:
- Developmental Biology
- Molecular Biology
- Genetics
Background:
- Evaluating combinatorial gene expression in whole embryos requires high spatial resolution.
- Existing methods may lack efficiency or scalability for multiplexed analysis.
Purpose of the Study:
- To present a method combining multiplexed fluorescent hybridization chain reaction (HCR) and advanced imaging for analyzing gene expression in mouse embryos.
- To demonstrate the application of this technique in studying craniofacial patterning and neural development.
Main Methods:
- Utilized DNA probes targeting specific mRNA sequences to initiate HCR amplification.
- Employed orthogonal initiators for spectrally distinct fluorophore labeling of multiple targets.
- Performed simultaneous in situ amplification of all target mRNAs.
Main Results:
- Achieved unprecedented spatial resolution in evaluating combinatorial gene expression patterns.
- Demonstrated simultaneous detection of three mRNA targets (Tg(egfp), Twist1, Pax2) in mouse embryos.
- Showcased the technique's applicability to complex developmental studies.
Conclusions:
- Multiplexed fluorescent HCR coupled with advanced imaging is a powerful tool for high-resolution gene expression analysis in whole embryos.
- This method allows for efficient and scalable investigation of cellular heterogeneity and tissue complexity during development.
